Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100360
Name   oriT_pKC394 in_silico
Organism   Escherichia coli O25b:H4-ST131
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_014231 (41344..42002 [+], 659 nt)
oriT length   659 nt
IRs (inverted repeats)      IR1: 198..207, 210..219  (ATTGGGTGTT..AATACCTAAT)
 IR2:318..323, 329..334  (AAAAAA..TTTTTT)
  IR3: 392..401, 404..413  (GTATTCATGC..GCATGAATAC)
Location of nic site      300..301
Conserved sequence flanking the
  nic site    		  GGTGT|ATAGC
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 659 nt

>oriT_pKC394
AGCGCCGCAGATAATCTGACCGATTACCTCCTGAAACCAGGTCTATATAGGCCAAAAGTTCATCTGATACTTTTGCGGTTATTATTGGCATTCAGTCCTCACATTGTGCATTTCTTAAACAAAAAATTGGGATCTAACCAGCTGAAATCTTAGTATTACCAAAGTAATAAAGCAAACTCATTATAAAACAATGAGTTATTGGGTGTTTTAATACCTAATTATTACCGGATATTGACGCTATTTATTTTTTTATTTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAGGAGCGAACTACGTAGGTTAAGGACTAACTGGCTAAAAAGCGTTCAATATTCCGTATTCATGCTTGCATGAATACCAGTACAACACTATTACAACAAAAGTACATCAAAATTACATCAAAATTACATCACTTGAAGGTTGACAGTACAACAGAATTACATCATTATCTGGTCATGAGGTAGCCAGTACAACAAAAGTACATCAAAAATACATCATAAATACATCATAAATACATCAGAAATACATCAAAATTACATCATTCTAAATGAGGGTACTATGAAGCCCAAAAGTATCAGGGCGGCACTTCAGTTGATGTTGCCGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   431 GenBank   YP_003717510
Name   TraI_pKC394 insolico UniProt ID   Q0ZKV1
Length   1078 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1078 a.a.        Molecular weight: 120163.41 Da        Isoelectric Point: 6.5766

>YP_003717510.1 TraI (plasmid) [Escherichia coli O25b:H4-ST131]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATIADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKKEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
ISGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQGLTCDRVLFNIDTKSLTTSKDVFYVGISRARHEVEIFTDDKKSLASSVS
RDSPKTTAAEIDRFFGLEARFKDIGRDTSLETRSAEKGLPEATGESMAFNQKPDEHNMTTGTDYQPVSNA
EDAFHLKQNPMDDSVGLRRHEAQQNDAELAHDYAAADDQQWSAQEYADYEHYAEASDYDFDSSIYDDYAM
PQTSQAEQSHTGKEHTHEHEHEEGGHEI

  Protein domains


Predicted by InterproScan.

UvrD-like helicase C-terminal domain (UvrD_C_2)

(851-895)

TrwC relaxase (TrwC)

(16-287)

AAA domain (AAA_30)

(477-653)


  Protein structure


Source ID Structure
AlphaFold DB Q0ZKV1


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17191..27516

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS684_RS00075 12466..12816 + 351 Protein_14 WbuC family cupin fold metalloprotein -
HS684_RS00080 (pKC394-011) 12863..13738 - 876 WP_013188473 extended-spectrum class A beta-lactamase CTX-M-1 -
HS684_RS00085 (pKC394-012) 14096..14800 + 705 WP_013188471 IS6-like element IS26 family transposase -
HS684_RS00090 (pKC394-013) 14861..15058 - 198 WP_013188474 hypothetical protein -
HS684_RS00095 (pKC394-014) 15063..15704 - 642 WP_001694850 restriction endonuclease -
HS684_RS00100 (pKC394-015) 15760..15993 - 234 WP_001191790 hypothetical protein -
HS684_RS00105 (pKC394-016) 16107..16421 - 315 WP_001749965 TrbM/KikA/MpfK family conjugal transfer protein -
HS684_RS00110 (pKC394-017) 16384..16761 - 378 WP_000504250 hypothetical protein -
HS684_RS00115 (pKC394-018) 16777..17148 - 372 WP_011867773 H-NS family nucleoid-associated regulatory protein -
HS684_RS00120 (pKC394-019) 17191..17925 + 735 WP_000033783 lytic transglycosylase domain-containing protein virB1
HS684_RS00125 (pKC394-020) 17934..18215 + 282 WP_000440698 transcriptional repressor KorA -
HS684_RS00130 (pKC394-021) 18225..18518 + 294 WP_000209137 TrbC/VirB2 family protein virB2
HS684_RS00135 (pKC394-022) 18568..18885 + 318 WP_000496058 VirB3 family type IV secretion system protein virB3
HS684_RS00140 (pKC394-023) 18885..21485 + 2601 WP_001200711 VirB4 family type IV secretion/conjugal transfer ATPase virb4
HS684_RS00145 (pKC394-024) 21503..22216 + 714 WP_000749362 type IV secretion system protein virB5
HS684_RS00150 (pKC394-025) 22224..22451 + 228 WP_000734973 IncN-type entry exclusion lipoprotein EexN -
HS684_RS00155 (pKC394-026) 22467..23507 + 1041 WP_000886022 type IV secretion system protein virB6
HS684_RS00160 (pKC394-027) 23578..23736 + 159 WP_012561180 hypothetical protein -
HS684_RS00165 (pKC394-028) 23726..24424 + 699 WP_000646594 type IV secretion system protein virB8
HS684_RS00170 (pKC394-029) 24435..25319 + 885 WP_000735067 TrbG/VirB9 family P-type conjugative transfer protein virB9
HS684_RS00175 (pKC394-030) 25319..26479 + 1161 WP_000101712 type IV secretion system protein VirB10 virB10
HS684_RS00180 (pKC394-031) 26521..27516 + 996 WP_000128596 ATPase, T2SS/T4P/T4SS family virB11
HS684_RS00185 (pKC394-032) 27516..28049 + 534 WP_000731968 phospholipase D family protein -
HS684_RS00190 28218..29732 - 1515 Protein_37 Tn3-like element TnAs1 family transposase -
HS684_RS00195 (pKC394-033) 29798..30502 + 705 WP_001067855 IS6-like element IS26 family transposase -
HS684_RS00200 (pKC394-034) 30659..31219 - 561 WP_003124096 recombinase family protein -
HS684_RS00205 (pKC394-0341) 31484..32020 + 537 Protein_40 PAS domain-containing protein -

Host bacterium

ID   821 GenBank   NC_014231
Plasmid name   pKC394 Incompatibility group   IncN
Plasmid size   53207 bp Coordinate of oriT [Strand]   41344..42002 [+]
Host baterium   Escherichia coli O25b:H4-ST131

Cargo genes

Drug resistance gene   aph(4)-Ia, mph(A), blaCTX-M-1, blaCTX-M-65
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -